HHsearch alignment for GI: 254780766 and conserved domain: TIGR02168
>TIGR02168 SMC_prok_B chromosome segregation protein SMC; InterPro: IPR011890 The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases . All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression . The smc gene is often associated with scpB (IPR005234 from INTERPRO) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle , , .; GO: 0005515 protein binding, 0005524 ATP binding, 0005694 chromosome.
Probab=99.93 E-value=2.5e-25 Score=184.54 Aligned_cols=144 Identities=23% Similarity=0.299 Sum_probs=112.3
Q ss_pred EEEEEEEECCCCH-HHEEEECCCCEEEEECCCCCCHHHHHHHHHHHC---CCCCCCCCCHHHHHHCCCCCE-----EEEE
Q ss_conf 8999999223254-553673279879998689986444899999972---886666787368874898320-----5898
Q gi|254780766|r 6 KIKFLNISEFRNY-ASLRLVFDAQHTIFVGDNGVGKTNILEAISFLS---PGRGFRRASYADVTRIGSPSF-----FSTF 76 (375)
Q Consensus 6 ~i~~l~i~nFR~~-~~~~i~f~~~~n~i~G~NG~GKT~iLEAI~~l~---~gksfR~~~~~~li~~~~~~~-----~~~~ 76 (375)
T Consensus 1 ~Lk~l~l~GFKSFaD~t~i~F~~g~TgiVGPNGcGKSNi~DAiRWVLGEqSak~LRg~~M~DVIF~Gs~~Rkp~~~AeV~ 80 (1191)
T TIGR02168 1 RLKKLELAGFKSFADPTTINFDKGITGIVGPNGCGKSNIVDAIRWVLGEQSAKALRGGKMEDVIFNGSETRKPLSLAEVE 80 (1191)
T ss_pred CCCEEEECCCCCCCCCEEEEECCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCEEEEE
T ss_conf 96135761210135304786178527986279987001899999860033477734689995563488777657700689
Q ss_pred EEECCCC--------CCEEEEEEEECCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCHHHC---------CCCCCH
Q ss_conf 8862853--------2002667530024-663332112577433321012333452021001100---------126872
Q gi|254780766|r 77 ARVEGME--------GLADISIKLETRD-DRSVRCLQINDVVIRVVDELNKHLRISWLVPSMDRI---------FSGLSM 138 (375)
Q Consensus 77 ~~~~~~~--------~~~~~~~~~~~~~-~~~~k~~~~n~~~~~~~~~l~~~l~~v~~~p~~~~l---------i~~~p~ 138 (375)
T Consensus 81 L~fdN~d~~l~~~y~~y~Ei~itRr~~Rg~GeS-eY~iN~~~cRL-kDI~dLF~dtGlG~~sysII~QG~I~~i~~aKPe 158 (1191)
T TIGR02168 81 LVFDNSDGLLPGQYADYSEISITRRLYRGDGES-EYFINGQPCRL-KDIQDLFLDTGLGKRSYSIIEQGKISEIIEAKPE 158 (1191)
T ss_pred EEEECCCCCCHHHHCCCCEEEEEEEEEECCCCC-EEEECCCCCHH-HHHHHHHHHCCCCCCCCEEECCCCHHHHHCCCHH
T ss_conf 888558883512113677178998887458644-04557750137-7799887322788654323034305565249968
Q ss_pred HHHHHCCC--CCCCC
Q ss_conf 34121010--00135
Q gi|254780766|r 139 ERRRFLDR--MVFAI 151 (375)
Q Consensus 139 ~RR~flD~--~i~~~ 151 (375)
T Consensus 159 erR~i~EEAAGisKY 173 (1191)
T TIGR02168 159 ERRAIFEEAAGISKY 173 (1191)
T ss_pred HHHHHHHHHCCHHHH
T ss_conf 999998872135788